Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HLDNKGNC_5 | 671169 | 672338 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| HLDNKGNC_5 | 497851 | 499053 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| HLDNKGNC_5 | 478880 | 479734 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| HLDNKGNC_12 | 338514 | 339434 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| HLDNKGNC_12 | 325182 | 326621 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| HLDNKGNC_12 | 275506 | 276099 | tmrB | ARO:3003059 | tmrB | 97.46 | 100.00 | AL009126.3 |
| HLDNKGNC_7 | 41673 | 41990 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HLDNKGNC_7 | 41335 | 41673 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HLDNKGNC_12 | 29099 | 30742 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| HLDNKGNC_6 | 27283 | 29853 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| HLDNKGNC_8 | 327146 | 328522 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.91 | 100.00 | X08034 |
| HLDNKGNC_5 | 478880 | 479732 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| HLDNKGNC_12 | 338514 | 339434 | mph(K) | Spiramycin, Telithromycin | 97.83 | 100.00 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HLDNKGNC_8 | 327149 | 328522 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_003242953.1 |
| HLDNKGNC_12 | 338517 | 339434 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| HLDNKGNC_12 | 29099 | 30739 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| HLDNKGNC_5 | 478880 | 479731 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| HLDNKGNC_8 | 324684 | 325202 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| HLDNKGNC_5 | 1019345 | 1021942 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 100.00 | WP_087347987.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| HLDNKGNC_14 | 246840 | 248021 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| HLDNKGNC_14 | 245215 | 246357 | capA | 0.0 | Capsule | Immune modulation | 99.47 | 100.00 | NP_391469 |
| HLDNKGNC_5 | 913472 | 914113 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.38 | 100.00 | NP_390062 |
| HLDNKGNC_9 | 113134 | 113919 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| HLDNKGNC_9 | 109298 | 110236 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| HLDNKGNC_14 | 246376 | 246825 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| HLDNKGNC_9 | 102142 | 109278 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.22 | 100.00 | NP_391076 |
| HLDNKGNC_5 | 1067129 | 1068892 | dep/capD | 0.0 | Capsule | Immune modulation | 98.81 | 100.00 | NP_389723 |
| HLDNKGNC_9 | 111912 | 113108 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| HLDNKGNC_9 | 110264 | 111883 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391078 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| HLDNKGNC_3 | 28048 | 26912 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HLDNKGNC_15 | 11189 | 10320 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HLDNKGNC_7 | 355161 | 355937 | CodY | 5.67e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HLDNKGNC_14 | 88249 | 88818 | ClpP | 2.43e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HLDNKGNC_11 | 107464 | 107072 | spxA1 | 2.45e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HLDNKGNC_11 | 107464 | 107072 | spx | 1.46e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HLDNKGNC_4 | 20677 | 20919 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HLDNKGNC_12 | 78742 | 78545 | CspA | 1.85e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HLDNKGNC_11 | 350675 | 350869 | CspB | 3.52e-27 | cold shock protein | 83.08 | 98.48 | CAD00094 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| HLDNKGNC_13 | 884 | 1051 | Col(SD853) | 168 / 194 | 86.90 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HLDNKGNC_1 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_2 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_3 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_4 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_5 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_6 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_7 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_8 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_9 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_10 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_11 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_12 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_13 | 1.0 | 0.0 | 1.0 |
| HLDNKGNC_14 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_15 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_16 | 1.0 | 0.0 | 1.0 |
| HLDNKGNC_17 | 0.0 | 1.0 | 0.0 |
| HLDNKGNC_18 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HLDNKGNC_5 | 285120 | 310491 | False | Myoviridae | VOG0796, VOG0720, VOG4555, VOG4553, VOG0815, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753, VOG0136, VOG4574, VOG6116 |
| HLDNKGNC_5 | 865714 | 883384 | False | Siphoviridae | VOG3699, VOG0221, VOG7734, VOG0720, VOG4555, VOG4572, VOG4713, VOG9219, VOG4910, VOG5042 |
| HLDNKGNC_7 | 3701 | 11842 | False | Myoviridae | VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| HLDNKGNC_7 | 571173 | 586175 | False | Unknown | VOG5070, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312 |
| HLDNKGNC_7 | 593850 | 605365 | False | Myoviridae / Siphoviridae | VOG6940, VOG9713, VOG9219, VOG5495, VOG6036, VOG7134, VOG10940, VOG5721, VOG5779, VOG5722, VOG4581 |
| HLDNKGNC_11 | 5355 | 15277 | False | Siphoviridae | VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)